1. 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources (http://popcorn.maizegdb.org) Jack M. Gardiner Poster P897

2. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 2 http://popcorn.maizegdb.org A set of project and sequence-indexed data searching resources

3. POPcorn: Project Portal for corn www.popcorn.maizegdb.org 3

4. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 4 Project Objectives: Difficult to find all online resources relevant to ones research Project Search Project Objectives: Difficult to find all online resources relevant to ones research Project Search

5. POPcorn: Project Portal for corn www.maizegdb.org/POPcorn 5 Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST

6. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 6 Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Sequence-indexed data can be challenging to search Sequence-Indexed Data Search Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Sequence-indexed data can be challenging to search Sequence-Indexed Data Search

7. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 7 Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Sequence-indexed data can be challenging to search Sequence-Indexed Data Search Data and web resources can disappear after project completion Processes and scripts to migrate data to MaizeGDB Project Objectives: Difficult to find all online resources relevant to ones research Project Search Repeated BLAST searches at multiple sites POPcorn BLAST Sequence-indexed data can be challenging to search Sequence-Indexed Data Search Data and web resources can disappear after project completion Processes and scripts to migrate data to MaizeGDB

8. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 8 Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources

9. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 9

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11. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 11

12. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 12 Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources We need your help! submit projects not in our database send us corrections Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources We need your help! submit projects not in our database send us corrections

13. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 13 Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources Information presented for each project and resource We need your help! submit projects not in our database send us corrections Types of projects and resources: just about everything that is relevant to maize … except cultural, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/) Project Search Database of maize research projects and online resources Hand-curated and updated monthly; 97 projects, 128 resources Information presented for each project and resource We need your help! submit projects not in our database send us corrections Types of projects and resources: just about everything that is relevant to maize … except cultural, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/)

14. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 14 Two options for searching with a sequence Simple sequence to sequence search (BLAST) Sequenced index search (access biological resources associated with a sequence) Two options for searching with a sequence Simple sequence to sequence search (BLAST) Sequenced index search (access biological resources associated with a sequence)

15. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 15

16. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 16 BLAST against target sequence at multiple websites using Web Services Results can be returned via email BLAST against target sequence at multiple websites using Web Services Results can be returned via email

17. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 17 BLAST against target sequence at multiple websites using Web Services Results can be returned via email Contact us to add your target sequence or to set up a similar service BLAST against target sequence at multiple websites using Web Services Results can be returned via email Contact us to add your target sequence or to set up a similar service

18. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 18 Sequence-indexed data search Carries out complex searches One or more searches at once Sequence-indexed data search Carries out complex searches One or more searches at once

19. POPcorn: Project Portal for corn http://popcorn.maizegdb.org 19

20. 20 POPcorn: Project Portal for corn http://popcorn.maizegdb.org An example: steps taken to find a UniformMu stock containing a given mutation. 1.BLAST query sequence against NCBI GSS 2.Parse definition line to get UniformMu locus name 3.Get LOCUS record at MaizeGDB 4.Get VARIATION record(s) for that LOCUS at MaizeGDB 5.Get UniformMu STOCK records for each VARIATION at MaizeGDB 6.Construct links to MGC Stock Center for each stock found.

21. 21 POPcorn: Project Portal for corn http://popcorn.maizegdb.org An example: steps taken to find a UniformMu stock containing a given mutation. 1.BLAST query sequence against NCBI GSS 2.Parse definition line to get UniformMu locus name 3.Get LOCUS record at MaizeGDB 4.Get VARIATION records for that LOCUS at MaizeGDB 5.Get UniformMu STOCK records for each VARIATION at MaizeGDB 6.Construct links to MGC Stock Center for each stock found.

22. 22 POPcorn: Project Portal for corn http://popcorn.maizegdb.org Select a target database Input your sequence (split files larger than 20MB) Provide some information about your data Submit! uBLAST

23. 23 POPcorn: Project Portal for corn http://popcorn.maizegdb.org Monitor progress of your job You will receive an e-mail when your job is complete uBLAST

24. 24 POPcorn: Project Portal for corn http://popcorn.maizegdb.org Check your alignment on the MaizeGDB.org genome browser If the results look correct, submit to MaizeGDB.org uBLAST

25. 25 POPcorn: Project Portal for corn http://popcorn.maizegdb.org CViT – Chromosome Viewing Tool Displays features on chromosomes (linkage groups, pseudomolecules, chromosome arms, et cetera)

26. 26 POPcorn: Project Portal for corn http://popcorn.maizegdb.org CViT – Chromosome Viewing Tool

27. 27 POPcorn Principal Investigator: Carolyn Lawrence (USDA-ARS) Co-Principal Investigator: Taner Sen (USDA-ARS) Solution/Application Architect: Ethy Cannon (Iowa State) Programmer Analyst: Scott Birkett (Iowa State) Programmer Analyst: Bremen Braun (USDA-ARS) Curator: Jack Gardiner (Iowa State) POPcorn Principal Investigator: Carolyn Lawrence (USDA-ARS) Co-Principal Investigator: Taner Sen (USDA-ARS) Solution/Application Architect: Ethy Cannon (Iowa State) Programmer Analyst: Scott Birkett (Iowa State) Programmer Analyst: Bremen Braun (USDA-ARS) Curator: Jack Gardiner (Iowa State) MaizeGDB/POPcorn team Poster P897